Sorry, i should have been a little more specific.
Pouchitis is caused by a bacterial overgrowth of 'bad' bacteria which causes all the issues. When you take the antibiotics you kill everything, good and bad, in theory at least. Sometimes the bacterial colonies will get lessened to the point where you aren't symptomatic anymore, but are still there. That's why they always tell you with antibiotics to take the full 2 week does to make sure everything is dead.
That's what I mean, you want to make sure the bad bacteria is gone completely before you try and repopulate with the good stuff (what's in the VSL).
Personally I think to give yourself the best chance with VSL you should start taking heavy doses about 2 days before coming off a two week stint with both flagyl and cipro (If they still work for you). If neither work for you, then after 2 weeks of an antibiotic treatment you know works.
As others have stated, it can take 30-45 days to get the bacterial re-growth established and balanced out. Common early symptoms while this process happen are gas and bloating, and sometimes increased frequency, but no blood.
I've had good results with VSL, but it doesn't work with everyone. Hopefully it does for you.